Contacts of the strand formed by residues 108 - 114 (chain B) in PDB entry 3FPK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B CYS* 3.5 3.7 - - - -
107B GLU* 1.3 81.1 + - - +
109B LEU* 1.3 60.3 + - - +
110B TRP* 3.4 29.7 + - + +
136B ASN* 2.9 35.9 + - + -
138B VAL* 3.9 18.2 - - + -
200B LEU* 4.1 11.0 - - + +
201B PRO* 4.8 2.5 + - - +
206B THR* 2.9 13.1 + - - -
207B SER* 3.3 7.6 - - - -
208B HIS 3.0 26.5 + - - +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 3.8 28.7 - - + -
103B VAL* 4.0 15.5 - - + -
106B CYS* 4.0 1.7 - - - -
107B GLU 4.2 0.2 - - - -
108B THR* 1.3 73.6 - - - +
110B TRP* 1.3 62.9 + - - +
111B MET* 4.0 16.3 + - + +
124B ILE* 6.1 0.4 - - + -
134B PHE* 3.9 26.9 - - + -
136B ASN 2.9 8.7 + - - -
137B LEU* 3.5 23.0 - - + -
138B VAL 2.9 26.1 + - - +
208B HIS* 3.8 15.7 - - + +
210B MET* 3.9 31.0 - - + -
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Residues in contact with TRP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B THR* 3.4 18.1 - - + +
109B LEU* 1.3 73.3 - - - +
111B MET* 1.3 57.7 + - - +
112B LEU* 4.0 11.2 - - + -
138B VAL* 3.6 32.3 - - + -
140B VAL* 4.3 1.1 - - + -
194B LEU* 4.1 11.7 - - + -
195B GLU* 4.3 10.1 - - + -
198B VAL* 3.8 27.1 - - + -
200B LEU* 3.4 33.7 - - + -
201B PRO 3.3 14.6 + - - -
202B MET* 3.4 34.3 - - + +
207B SER* 3.2 35.1 + - - -
208B HIS 2.9 12.1 + - - +
209B VAL* 3.5 14.1 - - + -
210B MET* 2.7 34.0 + - - +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 4.0 15.5 - - + +
110B TRP* 1.3 75.6 - - - +
112B LEU* 1.3 63.4 + - - +
121B TYR* 3.6 51.8 - - + -
124B ILE* 5.3 7.6 - - - -
125B LEU* 4.0 28.7 - - + -
137B LEU* 3.9 32.5 - - + -
138B VAL 2.8 28.6 + - - +
139B LEU* 3.6 6.2 - - + +
140B VAL 2.9 27.9 + - - +
166B LEU* 4.5 0.9 - - + -
210B MET* 3.8 11.4 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B TRP* 4.2 17.9 - - + -
111B MET* 1.3 77.9 - - - +
113B ALA* 1.3 60.8 + - - +
121B TYR* 2.8 19.4 + - - -
140B VAL* 3.6 34.8 - - + -
185B VAL* 4.0 24.7 - - + -
189B ILE* 4.2 14.4 - - + -
194B LEU* 4.7 3.1 - - + -
202B MET* 4.4 3.8 - - + -
209B VAL* 3.6 23.1 - - + -
210B MET 2.8 18.0 + - - +
211B LEU* 3.5 6.2 - - + -
212B CYS 3.0 15.9 + - - -
217B MET* 4.1 13.0 - - + -
221B THR* 4.2 9.0 - - + -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU* 1.3 75.5 - - - +
114B THR* 1.4 62.5 + - - +
117B ALA 3.5 31.6 - - - +
118B ILE* 3.6 14.8 - - + +
121B TYR* 3.6 12.8 - - + -
140B VAL* 3.0 12.8 + - - +
141B HIS* 3.7 1.3 - - - -
142B ALA* 2.9 27.5 + - - +
185B VAL* 5.6 1.8 - - - +
212B CYS 3.3 6.3 - - - -
217B MET* 4.2 1.7 - - - +
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Residues in contact with THR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA* 1.4 74.6 - - - +
115B GLY* 1.3 67.9 + - - +
116B THR 3.2 0.5 + - - -
117B ALA* 2.8 18.9 + - - +
142B ALA* 3.3 17.0 - - + +
212B CYS 3.3 4.2 + - - -
213B GLY* 3.6 1.2 - - - -
214B ASN* 2.9 33.6 + - + +
217B MET* 3.7 39.0 - - + -
248B TRP* 5.6 0.5 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il